Get genotypes matrix (counts of reference allele) from a GenABEL gwaa-data, vcfR object or an object imported using seqminer

Get genotypes matrix (counts of reference allele) from a GenABEL gwaa-data, vcfR object or an object imported using seqminer

get_genotypes(x, ind_names = NULL, marker_names = NULL)

Arguments

x	a gwaa-data, a vcfR object or a genotype matrix loaded using seqminer
ind_names	names of individuals to extract
marker_names	names of markers to extract

Value

genotype matrix ind x marker with counts of the reference allele

Details

if marker_names is not provided, all markers present in x will be returned similarly, if ind_names is not present all individuals will be returned NOTE: beware that the genotype matrix returned contains counts of a reference allele which NOT NECESSARILY is the minor allele. Use gwasim::validate_maf() to be sure you are working with the minor alllele counts. Also, note that removing individuals may change allele frequencies and thus different alllele will be considered minor.

Author

Marcin Kierczak <marcin.kierczak@scilifelab.se>